CCP5 Software DL_POLY contributes to explanation of archeological quandary
18 Nov 2019
No
- Dawn Geatches

 

 

by confirming that fossilized ostrich eggshells preserve proteins bound to the solid surface of the eggshell.

Yes

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Are you wondering where to find some very old proteins? If so, look no further than your nearest 

fossilized ostrich eggshell in equatorial Africa, for it's there that protein preserved for 3.8 million years has been found. That’s over 5 times older than the 700,000 year old DNA found in the Arctic. This might seem strange given the higher, tropical temperatures in Africa, and the effect that time and temperature have on the degradation of biomolecules.​ 


Addressing this conundrum, archaeologists (led by Prof Matthew Collins) at the University of York hypothesized that proteins could survive intact if bound to a solid surface such as an eggshell.​ For example, within an ostrich's womb, '..several proteins are responsible for assembling the minerals that make up the ostrich eggshell. These proteins become trapped tightly within the mineral crystals themselves.'In the case of ostrich eggshells, this mineral is calcium carbonate - calcite - (CaCO3​).


Researchers from universities across the world (e.g. Denmark, US, South Africa and the UK) ​used a combination of experimental and computational methods to determine how the eggshell protected biomolecules over millenia. Researchers from the University of Sheffield used computational classical molecular dynamics to​ probe the atomistic binding geometries between the calcite and protein (similar to this research.) They used the Collaborative Computational Project 5’s (CCP5) classical molecular dynamics program – DL_POLY – and discovered​ that the part of the protein that binds most strongly to the calcite surface of the eggshell, is most likely to remain preserved.ostrich_protein_calcite.jpg



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     1​​ https://elifesciences.org/articles/17092#abstract​​                      Figure (from paper shown to the left) showing survival of                                                                                                                     protein constituents (i.e. peptides) with images from the                                                                                                                       DL_POLY simulations shown at the top​


Although fragments of amino acids have been found in much older fossils, whole protein sequences contain more valuable information, such as the function of the protein. This can lead to robust evolutionary information obtained from ‘biological barcodes’, an improvement on the previous need to resort to inferring evolutionary relationships.​


Atomistic modelling methods are powerful tools enabling us to explore the atomic-level interactions of a wide range of systems, and they work especially well in combination with experimental methods, as in the example given above. For further information about atomistic modelling carried out within the Chemistry Group at STFC, click here​

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Some of the material used in this case study was adapted from a BBC News & Environment article 


   


      





 




















Contact: Geatches, Dawn (STFC,DL,SC)